Gene Lists

The Immunology Database and Analysis Portal (ImmPort) system was developed under the Bioinformatics Integration Support Contract (BISC) Phase II by the Northrop Grumman Information Technology Health Solutions team for the NIH, NIAID, and DAIT. The principal investigator of the BISC project is Dr. Richard Scheuermann at University of Texas Southwestern Medical Center. The list of immunologically related genes in ImmPort is a collection of ~6,000 human genes, which was formed with the goal of retrieving all genes that have immune system-related functions. This list was generated using automatic searches of EntrezGene and Gene Ontology records using immunology-related keywords. The list was then manually curated by immunology experts examining various literature sources.

This gene list, of 1,535 immune genes (December 7, 2014), is derived from the IRIS online database of known human defense genes (note that the IRIS database does not seem to be available anymore).
These genes were curated by IRIS from the literature where an immune gene was defined as a complete gene that produces a functional transcript and demonstrates at least one of the following defense
characteristics: (i) Known or putative function in innate or adaptive
immunity, (ii) Participates in the development or maturation of immune
system components (iii) Induced by immunomodulators, (iv) Encodes a protein
expressed primarily in immune tissues, (v) Participates in an immune
pathway that results in the expression of defense molecules, (vi)
Produces a protein that interacts directly with pathogens or their products.

This gene list is derived from the Septic Shock group
which is a collaboration between ISB, TSRI and Rockefeller University
research groups.
The list includes 1,448 genes with potential relevance
to macrophage response to microbial stimulation (December 7, 2014). The list combines
genes with significant expression changes under stimulation with LPS,
and genes coding for proteins known to interact in the TNFa/NF-kB
signaling pathway.

This gene list was derived from in house curation of the p38, ERK, JNK signaling pathways (Raymond Lo and Fiona Roche) and the NFKB transcriptional regulatory module (Jenn Gardy). It contains 761 genes (December 7, 2014); members of the TNF-alpha and IFN-alpha signaling pathway derived from Transpath data were also included.

This study used microarrays to analyse changes in blood leukocyte gene expression patterns in human subjects receiving an inflammatory stimulus (bacterial endotoxin). Here they evaluate the genome-wide response to systemic inflammation in the context of a fully predictable recovery. Gene expression in whole blood leukocytes was determined immediately before and at 2, 4, 6, 9 and 24 h after the intravenous administration of bacterial endotoxin to four healthy human subjects. Four additional subjects were studied under identical conditions but without endotoxin administration. A total of 3,714 unique genes that were significantly perturbed after bacterial endotoxin administration were identified using significance analysis of microarrays (SAM) (multiclass response), with an estimated false discovery rate of <0.1% on the basis of 1,000 permutations. Genes showing significant transcriptional changes were verified in another microarray study where an additional six healthy subjects (one female and five males) were administered 2 ng kg-1 (body weight) endotoxin, and blood samples were collected before (0 h) and after (2 and 6 h) endotoxin infusion.

Immunology-related genes were collected from research articles, textbooks and electronic information sources. The list contains genes that are directly involved in immunological processes. In addition to clearly defined groups, such as clusters of differentiation (CD) molecules, chemokines and their receptors, other essential genes were included. Genes were included when they are undoubtedly needed for immunity. Immunodeficiency-related genes were taken from the ImmunoDeficiency Resource and IDbases. Proteins that are expressed in nearly all cells were excluded, although their functions may also be needed in immunity related cells and tissues. Only full-length genes were included; thus, the gene segments of immunoglobulins, B and T cell receptors and major histocompatibility complexes (MHCs) were excluded. In the case of signaling molecules, only those involved in immunity-related cascades were included. Altogether, 844 genes were selected for InnateDB (December 7, 2014).

InnateDB is being developed jointly by the Brinkman Laboratory (Simon Fraser University, British Columbia, Canada),
the Hancock Laboratory (University of British Columbia, Vancouver, British Columbia)
and the Lynn EMBL Australia Group (South Australian Health & Medical Research Institute and Flinders University, Adelaide, Australia).

Funding is currently provided by Allergen and EMBL Australia. Previous funding has been provided by Genome Canada, the Foundation for the National Institutes of Health
through the Grand Challenges in Global Health initiative and by Teagasc. InnateDB curated interactions are licensed under the Design Science License. All other data is licensed under the terms of the originating database.
Contact: innatedb-mail@sfu.ca